Adrien Schahl

Our Story about ADAM10 modulation by PS lipids found its home in Advanced Science !
Many thanks to all co-authors for an amazing collaboration.

Membrane-associated effluxosomes coordinate multi-metal resistance in Mycobacterium tuberculosis - The EMBO Journal Bacterial pathogens must withstand metal-induced stress during infection, yet the mechanisms by which they sense and respond to toxic metal ions remain incompletely understood. Here, we uncover a prev...

🎉 𝐄𝐱𝐜𝐢𝐭𝐞𝐝 𝐭𝐨 𝐬𝐡𝐚𝐫𝐞 𝐨𝐮𝐫 𝐧𝐞𝐰 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐢𝐧 𝐓𝐡𝐞 𝐄𝐌𝐁𝐎 𝐉𝐨𝐮𝐫𝐧𝐚𝐥!

After 8 months of revision, our work is now online: shorturl.at/WHmFq

We uncover a previously unrecognized way that 𝑀𝑦𝑐𝑜𝑏𝑎𝑐𝑡𝑒𝑟𝑖𝑢𝑚 𝑡𝑢𝑏𝑒𝑟𝑐𝑢𝑙𝑜𝑠𝑖𝑠 survives toxic metal stress during infection.
...

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Thanks for the answer. I'm always skeptical with LLMs answers to scientific questions, so I'll also keep this example in mind.

May I ask which ones you've asked to ? Personal experience : Notebook LLM has been fairly helpful in certain situation for me to understand quite complicated papers, so I would like to know if this is one of them.

Expected but still unpleasant, no MSCA funding for the upcoming year. According to others, even 96% wasn't enough in certain cases, which is completely mind blowing.

#compchem #compchemsky Our paper in J. Phys. Chem. Lett.: "Accelerating Molecular Dynamics Simulations with Foundation Neural Network Models using Multiple Time-Step and Distillation" made it to one of the covers! pubs.acs.org/doi/full/10....

Now out in @chemicalscience.rsc.org ! First paper by Léna Triestram in our group, “Identifying phase transitions in Zeolitic Imidazolate Frameworks” by advanced #compchem methods. #chemsky doi.org/10.1039/D5SC...

Moi y a pas longtemps on m'a dis " Dear PROFESSOR " hein 😎

Small step, but we take the change

Hey @lindorfflarsen.bsky.social we didn't choke out boxing day 🤩

#compchem #compbio Last preprint of the year: "Fast, systematic and robust relative binding free energies for simple and complex transformations : dual-LAO".
arxiv.org/abs/2512.17624
Great work by N. Ansari. @qubit-pharma.bsky.social .
Another nice collab with J. Hénin.

😍😍
Allez c'est bon je relance wind waker

GitHub - FeNNol-tools/FeNNol-PMC: FeNNol Pretrained Models Collection FeNNol Pretrained Models Collection. Contribute to FeNNol-tools/FeNNol-PMC development by creating an account on GitHub.

💫 We just released the weights of the #FeNNixBio1 foundation machine learning model for drug design! 💫

Weights: github.com/FeNNol-tools...
FeNNol code: github.com/FeNNol-tools...
The models are distributed under the open source ASL license (non-commercial academic research). #compchem #compbio

Bon courage, même chose ici avec le CNRS 🤞

Je te trouve très ronchon, on est probablement sur un article incroyable, dont nous ne mesurons pas la portée 🤡
Tain c'est affligeant 😂

Automatic machine learning model for enhanced partition and identification of breast disorders in breast MRI scan The rapid identification and categorisation of breast cancers using low-contrast MRI images presents a significant challenge due to the disease’s prevalence among women of all ages. Nowadays, it is...

Cet article cité 156 fois en 2025, impressionnant, ça doit vraiment être une révolution dans le milieu 🤡
Mais apparemment, ce n'est qu'en Inde qu'on s'est rendu compte de la révolution qu'il engendre, vu que les citations viennent exclusivement de la bas

Et bah... Publier sur la prédiction de la pollution de l'air, la détection des cancer des poumons, la protection contre les attaques DDoS, le traitement de la depression, les miRNAs, le net, les photons, faut reconnaitre qu'il est polyvalent 😂

Sticky Salts: Overbinding of Monovalent Cations to Phosphorylations in All-Atom Force Fields Phosphorylation is a major post-translational modification that is involved in the regulation of the dynamics and function of intrinsically disordered proteins (IDPs). We recently characterized a phen...

New paper is out !
We show that all classical phosphorylation forcefields that we tested lead to an overbinding of phosphate groups to bulk sodium (Na+) and potassium (K+) cations.

This assessment has serious implications for MD simulations of phosphorylated proteins !

doi.org/10.1021/acs....

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42...

To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.

With our start this season the boxing day is my worst nightmare so far 😩
But I recognise that I'll relax until then if we win this weekend against Chelsea.

😂 the ghost of previous seasons upon us 😬

Félicitations 🎉🎉🎉

Across (Conformational) Space and (Relaxation) Time: Using Coarse-Grain Simulations to Probe the Intra- and Interdomain Dynamics of the Tau Protein The biological importance of intrinsically disordered proteins (IDPs) has been established for over two decades, yet these systems remain difficult to characterize, as they are better described by conformational ensembles instead of a single reference structure for their folded counterparts. Tau is a prominent member of the IDP family, which sees its cellular function regulated by multiple phosphorylation sites and whose hyperphosphorylation is involved in neurodegenerative diseases such as Alzheimer’s. We used coarse-grain MD simulations with the CALVADOS model to investigate the conformational landscape of tau without and with phosphorylations. Characterizing the local compactness of IDPs allows us to highlight how disorder comes in various flavors, as we can define different domains along the tau sequence. We define the IDP’s Statistical Tertiary Organization (STO) as the average spatial arrangements of domains, which constitute an extension of the tertiary structure of folded proteins. We also use IDP-specific metrics to characterize the local curvature and flexibility of tau. Comparing the local flexibilities with T2 relaxation times from NMR experiments, we show how this metric is related to the protein dynamics. A curvature and flexibility pattern in the repeat domains can also be connected to tau binding properties, without having to explicitly model the protein’s interaction partner. Finally, we rediscuss the original paperclip model that describes the spatial organization of tau and how phosphorylations impact it. The resulting changes in the protein intradomain and interdomain interaction pattern allow us to propose experimental setups to test our hypothesis.

"Across (Conformational) Space and (Relaxation) Time", @marienj.bsky.social's latest work, is now out in J. Phys. Chem. B @pubs.acs.org. In this paper, we used coarse-grain simulations with the CALVADOS model to investigate the dynamics of a large IDP.
pubs.acs.org/doi/10.1021/...

An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies www.biorxiv.org/content/10.1...

If you click on dots you have the structure and description of the protein on the right of the screen

C'est beaucoup trop cool, j'me balade d'ilot en ilot comme j'me balade dans Zelda TOTK 😂

🤞

Il n'a pas eu besoin d'autant sur les dernières présidentielles américaines, donc rien ne laisse penser qu'il va s'arrêter la